Stress can change the balance of bacteria that naturally live in the gut, these bacteria affect immune function, and may help explain why stress deregulates the immune response. Exposure to stress led to changes in composition, diversity and number of gut microorganisms. The bacterial communities in the intestine became less diverse, and had greater numbers of potentially harmful bacteria, such as Clostridium. These changes can have profound implications for physiological function. The gut microorganisms may play a role in innate immunological stress responses because, gut bacteria have been linked to diseases like inflammatory bowel disease, and even to asthma.

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